Mercurial > repos > thomaswollmann > color_deconvolution

annotate color_deconvolution.py @ 4:a35141611262 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 2a8ca0fcc48586b1fcb3ae5ca42c6f97f72c588e
author thomaswollmann
date Sat, 11 Feb 2017 17:29:02 -0500
parents 3b2341714506
children b1a42e192603
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101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
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1 import argparse
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
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2 import sys
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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3 import warnings
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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4 import numpy as np
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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5 import skimage.io
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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6 import skimage.color
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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7 import skimage.util
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3b2341714506 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 92068c64f9a6c3cf59f756b9efc2d561196c6873
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8 from sklearn.decomposition import PCA, NMF, FastICA, FactorAnalysis
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10 convOptions = {
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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11 'hed2rgb' : lambda img_raw: skimage.color.hed2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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12 'hsv2rgb' : lambda img_raw: skimage.color.hsv2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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13 'lab2lch' : lambda img_raw: skimage.color.lab2lch(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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14 'lab2rgb' : lambda img_raw: skimage.color.lab2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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15 'lab2xyz' : lambda img_raw: skimage.color.lab2xyz(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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16 'lch2lab' : lambda img_raw: skimage.color.lch2lab(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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17 'luv2rgb' : lambda img_raw: skimage.color.luv2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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18 'luv2xyz' : lambda img_raw: skimage.color.luv2xyz(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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19 'rgb2hed' : lambda img_raw: skimage.color.rgb2hed(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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20 'rgb2hsv' : lambda img_raw: skimage.color.rgb2hsv(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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21 'rgb2lab' : lambda img_raw: skimage.color.rgb2lab(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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22 'rgb2luv' : lambda img_raw: skimage.color.rgb2luv(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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23 'rgb2rgbcie' : lambda img_raw: skimage.color.rgb2rgbcie(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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24 'rgb2xyz' : lambda img_raw: skimage.color.rgb2xyz(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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25 #'rgb2ycbcr' : lambda img_raw: skimage.color.rgb2ycbcr(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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26 #'rgb2yiq' : lambda img_raw: skimage.color.rgb2yiq(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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27 #'rgb2ypbpr' : lambda img_raw: skimage.color.rgb2ypbpr(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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28 #'rgb2yuv' : lambda img_raw: skimage.color.rgb2yuv(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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29 #'rgba2rgb' : lambda img_raw: skimage.color.rgba2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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30 'rgbcie2rgb' : lambda img_raw: skimage.color.rgbcie2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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31 'xyz2lab' : lambda img_raw: skimage.color.xyz2lab(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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32 'xyz2luv' : lambda img_raw: skimage.color.xyz2luv(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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33 'xyz2rgb' : lambda img_raw: skimage.color.xyz2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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34 #'ycbcr2rgb' : lambda img_raw: skimage.color.ycbcr2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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35 #'yiq2rgb' : lambda img_raw: skimage.color.yiq2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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36 #'ypbpr2rgb' : lambda img_raw: skimage.color.ypbpr2rgb(img_raw),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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37 #'yuv2rgb' : lambda img_raw: skimage.color.yuv2rgb(img_raw),
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38
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39 'rgb_from_hed' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hed),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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40 'rgb_from_hdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hdx),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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41 'rgb_from_fgx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_fgx),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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42 'rgb_from_bex' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bex),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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43 'rgb_from_rbd' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_rbd),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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44 'rgb_from_gdx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_gdx),
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45 'rgb_from_hax' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hax),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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46 'rgb_from_bro' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bro),
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47 'rgb_from_bpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_bpx),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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48 'rgb_from_ahx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_ahx),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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49 'rgb_from_hpx' : lambda img_raw: skimage.color.combine_stains(img_raw, skimage.color.rgb_from_hpx),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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50
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51 'hed_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hed_from_rgb),
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52 'hdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hdx_from_rgb),
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53 'fgx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.fgx_from_rgb),
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54 'bex_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bex_from_rgb),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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55 'rbd_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.rbd_from_rgb),
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56 'gdx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.gdx_from_rgb),
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57 'hax_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hax_from_rgb),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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58 'bro_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bro_from_rgb),
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
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59 'bpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.bpx_from_rgb),
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60 'ahx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.ahx_from_rgb),
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61 'hpx_from_rgb' : lambda img_raw: skimage.color.separate_stains(img_raw, skimage.color.hpx_from_rgb),
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62
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63 'pca' : lambda img_raw: np.reshape(PCA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
2
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64 [img_raw.shape[0],img_raw.shape[1],-1]),
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65 'nmf' : lambda img_raw: np.reshape(NMF(n_components=3, init='nndsvda').fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
3b2341714506 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 92068c64f9a6c3cf59f756b9efc2d561196c6873
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66 [img_raw.shape[0],img_raw.shape[1],-1]),
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67 'ica' : lambda img_raw: np.reshape(FastICA(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
3b2341714506 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit 92068c64f9a6c3cf59f756b9efc2d561196c6873
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68 [img_raw.shape[0],img_raw.shape[1],-1]),
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69 'fa' : lambda img_raw: np.reshape(FactorAnalysis(n_components=3).fit_transform(np.reshape(img_raw, [-1, img_raw.shape[2]])),
0
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70 [img_raw.shape[0],img_raw.shape[1],-1])
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71 }
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72
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73 parser = argparse.ArgumentParser()
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
74 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
75 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
76 parser.add_argument('conv_type', choices=convOptions.keys(), help='conversion type')
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
77 args = parser.parse_args()
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
78
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
79 img_in = skimage.io.imread(args.input_file.name)[:,:,0:3]
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
80 res = convOptions[args.conv_type](img_in)
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
81 res[res<-1]=-1
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
82 res[res>1]=1
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
83
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
84 with warnings.catch_warnings():
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
85 warnings.simplefilter("ignore")
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
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86 res = skimage.util.img_as_uint(res) #Attention: precision loss
101d1347abd9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/color-deconvolution commit b405a7bf071e77b80e314e4a5c340af71fd63adf
thomaswollmann
parents:
diff changeset
87 skimage.io.imsave(args.out_file.name, res, plugin='tifffile')